Multiple sequence alignment - TraesCS4D01G213400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G213400 chr4D 100.000 3805 0 0 1 3805 366278253 366274449 0.000000e+00 7027
1 TraesCS4D01G213400 chr4D 97.482 556 14 0 1 556 428537919 428537364 0.000000e+00 950
2 TraesCS4D01G213400 chr4D 96.583 556 19 0 1 556 436929699 436929144 0.000000e+00 922
3 TraesCS4D01G213400 chr4D 94.086 558 31 2 1 558 251555796 251555241 0.000000e+00 846
4 TraesCS4D01G213400 chr4D 94.192 551 31 1 1 551 217328136 217328685 0.000000e+00 839
5 TraesCS4D01G213400 chr4D 85.479 303 36 6 1996 2298 366274796 366274502 3.690000e-80 309
6 TraesCS4D01G213400 chr4D 85.479 303 36 6 3458 3752 366276258 366275956 3.690000e-80 309
7 TraesCS4D01G213400 chr4B 96.406 2254 68 4 671 2917 450863585 450861338 0.000000e+00 3701
8 TraesCS4D01G213400 chr4B 88.760 605 52 10 2970 3569 450861254 450860661 0.000000e+00 726
9 TraesCS4D01G213400 chr4B 86.149 296 33 2 3465 3752 450862248 450861953 2.850000e-81 313
10 TraesCS4D01G213400 chr4B 90.000 200 14 5 3612 3805 450860123 450859924 1.750000e-63 254
11 TraesCS4D01G213400 chr4B 88.991 109 12 0 1996 2104 450860773 450860665 6.630000e-28 135
12 TraesCS4D01G213400 chr4A 94.804 2367 100 12 556 2911 98777720 98780074 0.000000e+00 3668
13 TraesCS4D01G213400 chr4A 85.390 308 37 6 3453 3752 98779154 98779461 2.850000e-81 313
14 TraesCS4D01G213400 chr4A 92.135 89 4 3 2922 3008 98780883 98780970 5.160000e-24 122
15 TraesCS4D01G213400 chr3D 96.948 557 17 0 1 557 374016445 374015889 0.000000e+00 935
16 TraesCS4D01G213400 chr6D 94.424 556 31 0 1 556 409005473 409006028 0.000000e+00 856
17 TraesCS4D01G213400 chr2D 94.434 557 30 1 1 556 435438045 435437489 0.000000e+00 856
18 TraesCS4D01G213400 chr2D 94.065 556 33 0 1 556 168962980 168963535 0.000000e+00 845
19 TraesCS4D01G213400 chr2D 93.829 551 32 2 1 551 80253103 80252555 0.000000e+00 828


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G213400 chr4D 366274449 366278253 3804 True 2548.333333 7027 90.319333 1 3805 3 chr4D.!!$R4 3804
1 TraesCS4D01G213400 chr4D 428537364 428537919 555 True 950.000000 950 97.482000 1 556 1 chr4D.!!$R2 555
2 TraesCS4D01G213400 chr4D 436929144 436929699 555 True 922.000000 922 96.583000 1 556 1 chr4D.!!$R3 555
3 TraesCS4D01G213400 chr4D 251555241 251555796 555 True 846.000000 846 94.086000 1 558 1 chr4D.!!$R1 557
4 TraesCS4D01G213400 chr4D 217328136 217328685 549 False 839.000000 839 94.192000 1 551 1 chr4D.!!$F1 550
5 TraesCS4D01G213400 chr4B 450859924 450863585 3661 True 1025.800000 3701 90.061200 671 3805 5 chr4B.!!$R1 3134
6 TraesCS4D01G213400 chr4A 98777720 98780970 3250 False 1367.666667 3668 90.776333 556 3752 3 chr4A.!!$F1 3196
7 TraesCS4D01G213400 chr3D 374015889 374016445 556 True 935.000000 935 96.948000 1 557 1 chr3D.!!$R1 556
8 TraesCS4D01G213400 chr6D 409005473 409006028 555 False 856.000000 856 94.424000 1 556 1 chr6D.!!$F1 555
9 TraesCS4D01G213400 chr2D 435437489 435438045 556 True 856.000000 856 94.434000 1 556 1 chr2D.!!$R2 555
10 TraesCS4D01G213400 chr2D 168962980 168963535 555 False 845.000000 845 94.065000 1 556 1 chr2D.!!$F1 555
11 TraesCS4D01G213400 chr2D 80252555 80253103 548 True 828.000000 828 93.829000 1 551 1 chr2D.!!$R1 550

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
870 874 1.032114 AGGGGCTTTGCAATCGTAGC 61.032 55.0 11.6 11.6 0.0 3.58 F
1719 1729 0.179000 CGAGCAGGCTATGGAAGGTT 59.821 55.0 0.0 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2010 0.319986 TATCACGTCGCACCTGCAAA 60.320 50.0 0.0 0.0 42.21 3.68 R
3437 4254 0.035458 GGAAGGGGATACTCCATGCG 59.965 60.0 0.0 0.0 38.59 4.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 4.574674 TGCTAGGATTGTTTGGAGATGT 57.425 40.909 0.00 0.00 0.00 3.06
324 325 1.056660 AAGACGACCATGGTGAAGGT 58.943 50.000 25.52 14.46 41.83 3.50
362 363 2.946329 GCTTGATCTCGAGACCTCTACA 59.054 50.000 19.30 8.49 0.00 2.74
441 442 5.163499 CGACCTTCTTAGCTTTATCCTGAGT 60.163 44.000 0.00 0.00 0.00 3.41
465 467 3.745799 TGGGCTCGATGACTGTTTTTAA 58.254 40.909 0.00 0.00 0.00 1.52
503 506 1.951209 TCTGTGTGGATCCTGCCTAA 58.049 50.000 14.23 0.00 0.00 2.69
575 578 7.651027 AAAAAGGAGCACTGCAATTCTATAT 57.349 32.000 3.30 0.00 0.00 0.86
639 643 5.421212 ACGAACACTAGTCGAGATTATCC 57.579 43.478 9.21 0.00 0.00 2.59
663 667 6.062749 CCATTCTCTTGTCTTGATGGATCAT 58.937 40.000 0.00 0.00 36.56 2.45
664 668 6.017026 CCATTCTCTTGTCTTGATGGATCATG 60.017 42.308 0.00 0.00 36.56 3.07
665 669 4.449131 TCTCTTGTCTTGATGGATCATGC 58.551 43.478 0.00 0.00 36.56 4.06
666 670 4.080751 TCTCTTGTCTTGATGGATCATGCA 60.081 41.667 0.00 0.00 36.56 3.96
667 671 4.788679 TCTTGTCTTGATGGATCATGCAT 58.211 39.130 0.00 0.00 36.56 3.96
704 708 6.149474 GCACTAGACTTGCTTGATTTTCCTTA 59.851 38.462 0.00 0.00 37.00 2.69
828 832 3.571571 CAATGTGCTGAATTGGACAGTG 58.428 45.455 4.07 4.07 44.66 3.66
870 874 1.032114 AGGGGCTTTGCAATCGTAGC 61.032 55.000 11.60 11.60 0.00 3.58
1014 1018 4.158786 AGGTGATCATGGAGTCCATAGAG 58.841 47.826 24.40 12.61 43.15 2.43
1015 1019 3.306641 GGTGATCATGGAGTCCATAGAGC 60.307 52.174 24.40 23.20 43.15 4.09
1019 1023 4.461450 TCATGGAGTCCATAGAGCTAGT 57.539 45.455 24.40 0.00 43.15 2.57
1134 1144 3.494048 CCCACTCTCTCCAGATATGCAAC 60.494 52.174 0.00 0.00 0.00 4.17
1245 1255 0.676184 AGTCCCGTGATCATGATCCG 59.324 55.000 28.61 27.40 37.02 4.18
1287 1297 1.999648 ATTCCAAGCTGAAACCTGCA 58.000 45.000 0.00 0.00 0.00 4.41
1612 1622 1.078918 CGCTCACTGAATCTGGGCA 60.079 57.895 0.00 0.00 0.00 5.36
1719 1729 0.179000 CGAGCAGGCTATGGAAGGTT 59.821 55.000 0.00 0.00 0.00 3.50
1723 1733 1.748591 GCAGGCTATGGAAGGTTCAGG 60.749 57.143 0.00 0.00 0.00 3.86
1842 1852 0.966179 TCTCGCTCAACTACCAGCAA 59.034 50.000 0.00 0.00 35.15 3.91
1904 1914 0.248134 GAGAACTGGATCGACGTCGG 60.248 60.000 35.05 21.82 40.29 4.79
1949 1959 1.331756 GATCCGCGCAACTCAATTCAT 59.668 47.619 8.75 0.00 0.00 2.57
2037 2047 1.248785 TACAGCTGGTGTCCGAGACC 61.249 60.000 19.93 7.79 40.94 3.85
2157 2167 2.982130 GTGAGCAGGTCCACGGAT 59.018 61.111 0.00 0.00 0.00 4.18
2403 2413 2.492090 CTCTTCCAGCCGAGGTCG 59.508 66.667 0.00 0.00 39.44 4.79
2412 2422 2.927580 GCCGAGGTCGTGGTTCAGA 61.928 63.158 0.00 0.00 37.74 3.27
2507 2517 2.821366 CGTGTGCTGGAGGATGGC 60.821 66.667 0.00 0.00 0.00 4.40
2532 2542 2.240500 CGCAGCCGGCAAGACTATC 61.241 63.158 31.54 6.31 45.17 2.08
2550 2560 0.687757 TCGAGTGGGAGATCAAGGGG 60.688 60.000 0.00 0.00 0.00 4.79
2661 2671 8.783660 TCACCATTGGAGAGTAGTAGAAATAT 57.216 34.615 10.37 0.00 0.00 1.28
2696 2707 7.883311 TGATATCTCGTACTGATAGAATGGTCA 59.117 37.037 3.98 6.21 31.03 4.02
2786 2797 6.168389 TCATGGTGATAATATGCTAGCACTG 58.832 40.000 22.07 0.68 38.10 3.66
2837 2851 2.304761 GGATTACACCAGGGACTCACAA 59.695 50.000 0.00 0.00 34.60 3.33
2863 2877 2.173569 ACCTGAAGATGAACCCATAGCC 59.826 50.000 0.00 0.00 32.09 3.93
2917 2931 4.995124 ACATGATACGGAGTCAACAGTAC 58.005 43.478 0.00 0.00 43.93 2.73
2918 2932 4.705507 ACATGATACGGAGTCAACAGTACT 59.294 41.667 0.00 0.00 43.93 2.73
2919 2933 4.959596 TGATACGGAGTCAACAGTACTC 57.040 45.455 0.00 0.00 43.93 2.59
2995 3810 3.655211 AGCCAGGCTTCCCACCAG 61.655 66.667 8.70 0.00 33.89 4.00
2996 3811 3.650950 GCCAGGCTTCCCACCAGA 61.651 66.667 3.29 0.00 0.00 3.86
2997 3812 2.673523 CCAGGCTTCCCACCAGAG 59.326 66.667 0.00 0.00 0.00 3.35
2999 3814 3.334054 AGGCTTCCCACCAGAGGC 61.334 66.667 0.00 0.00 38.09 4.70
3001 3816 3.650950 GCTTCCCACCAGAGGCCA 61.651 66.667 5.01 0.00 33.00 5.36
3030 3845 1.134788 GTATTGCACCGTCAGTAGCCT 60.135 52.381 0.00 0.00 0.00 4.58
3032 3847 2.167398 TTGCACCGTCAGTAGCCTCC 62.167 60.000 0.00 0.00 0.00 4.30
3033 3848 2.490217 CACCGTCAGTAGCCTCCG 59.510 66.667 0.00 0.00 0.00 4.63
3034 3849 2.044555 CACCGTCAGTAGCCTCCGA 61.045 63.158 0.00 0.00 0.00 4.55
3035 3850 1.749638 ACCGTCAGTAGCCTCCGAG 60.750 63.158 0.00 0.00 0.00 4.63
3036 3851 2.409651 CGTCAGTAGCCTCCGAGC 59.590 66.667 0.00 0.00 0.00 5.03
3037 3852 2.409651 GTCAGTAGCCTCCGAGCG 59.590 66.667 0.00 0.00 38.01 5.03
3038 3853 2.045242 TCAGTAGCCTCCGAGCGT 60.045 61.111 0.00 0.00 38.01 5.07
3039 3854 2.103143 CAGTAGCCTCCGAGCGTG 59.897 66.667 0.00 0.00 38.01 5.34
3040 3855 2.045242 AGTAGCCTCCGAGCGTGA 60.045 61.111 0.00 0.00 38.01 4.35
3041 3856 2.102553 GTAGCCTCCGAGCGTGAC 59.897 66.667 0.00 0.00 38.01 3.67
3042 3857 2.045242 TAGCCTCCGAGCGTGACT 60.045 61.111 0.00 0.00 38.01 3.41
3043 3858 2.407428 TAGCCTCCGAGCGTGACTG 61.407 63.158 0.00 0.00 38.01 3.51
3050 3865 1.285950 CGAGCGTGACTGGAGTTGA 59.714 57.895 0.00 0.00 0.00 3.18
3084 3899 2.857483 TCGAAAATGAGAACCCAAGCA 58.143 42.857 0.00 0.00 0.00 3.91
3096 3912 1.163554 CCCAAGCAGCTCTTTCTGTC 58.836 55.000 0.00 0.00 36.49 3.51
3130 3946 1.751563 GCCTATCTCTGTGAGCCCC 59.248 63.158 0.00 0.00 0.00 5.80
3134 3950 0.687757 TATCTCTGTGAGCCCCGCTT 60.688 55.000 0.00 0.00 39.88 4.68
3135 3951 2.249413 ATCTCTGTGAGCCCCGCTTG 62.249 60.000 0.00 0.00 39.88 4.01
3149 3965 2.037871 GCTTGGGGCGAAAAGAACA 58.962 52.632 0.00 0.00 0.00 3.18
3175 3991 8.773216 ACAAAGAAGAAAAGGGAGCTACTATAT 58.227 33.333 0.00 0.00 0.00 0.86
3178 3994 5.986501 AGAAAAGGGAGCTACTATATCCG 57.013 43.478 0.00 0.00 33.68 4.18
3184 4000 0.611062 AGCTACTATATCCGGCCGCA 60.611 55.000 22.85 4.78 0.00 5.69
3211 4028 1.271926 ACGCACAGAAAAAGGGGCTAT 60.272 47.619 0.00 0.00 0.00 2.97
3213 4030 2.231235 CGCACAGAAAAAGGGGCTATTT 59.769 45.455 0.00 0.00 0.00 1.40
3217 4034 5.279256 GCACAGAAAAAGGGGCTATTTTACA 60.279 40.000 1.64 0.00 29.93 2.41
3220 4037 6.070824 ACAGAAAAAGGGGCTATTTTACATGG 60.071 38.462 0.00 0.00 29.93 3.66
3222 4039 5.675684 AAAAGGGGCTATTTTACATGGTG 57.324 39.130 0.00 0.00 0.00 4.17
3242 4059 4.082733 GGTGGCACCAAAGAAACTAAGATC 60.083 45.833 31.26 0.00 38.42 2.75
3246 4063 5.185828 GGCACCAAAGAAACTAAGATCCAAT 59.814 40.000 0.00 0.00 0.00 3.16
3250 4067 8.359642 CACCAAAGAAACTAAGATCCAATCAAA 58.640 33.333 0.00 0.00 0.00 2.69
3290 4107 3.817647 AGAGAGGCTAAAAGCACACAAAG 59.182 43.478 0.78 0.00 44.75 2.77
3291 4108 2.887152 AGAGGCTAAAAGCACACAAAGG 59.113 45.455 0.78 0.00 44.75 3.11
3292 4109 2.623416 GAGGCTAAAAGCACACAAAGGT 59.377 45.455 0.78 0.00 44.75 3.50
3334 4151 1.063174 GCGCCAAAAATGCACACAAAA 59.937 42.857 0.00 0.00 0.00 2.44
3335 4152 2.476854 GCGCCAAAAATGCACACAAAAA 60.477 40.909 0.00 0.00 0.00 1.94
3336 4153 3.352652 CGCCAAAAATGCACACAAAAAG 58.647 40.909 0.00 0.00 0.00 2.27
3351 4168 6.876257 CACACAAAAAGAAGGAGCTACTCTAT 59.124 38.462 0.00 0.00 0.00 1.98
3357 4174 1.323412 AGGAGCTACTCTATGCGGTG 58.677 55.000 0.00 0.00 0.00 4.94
3359 4176 0.319125 GAGCTACTCTATGCGGTGGC 60.319 60.000 0.00 0.00 39.63 5.01
3388 4205 9.586435 CAAAGAAACTAAGATTCAACCAAGTTT 57.414 29.630 0.00 0.00 39.24 2.66
3402 4219 7.039882 TCAACCAAGTTTTTATACGCCAAAAA 58.960 30.769 0.00 0.00 33.61 1.94
3440 4257 1.170919 GGCTACTCTACCCGATCGCA 61.171 60.000 10.32 0.00 0.00 5.10
3445 4262 0.242286 CTCTACCCGATCGCATGGAG 59.758 60.000 10.32 12.17 0.00 3.86
3447 4264 1.202842 TCTACCCGATCGCATGGAGTA 60.203 52.381 10.32 3.29 0.00 2.59
3476 4293 1.601903 CTTTAGTTTGCAGGTGCGACA 59.398 47.619 9.93 0.00 45.83 4.35
3494 4311 3.193263 GACATGATACAGCTGGTGTCTG 58.807 50.000 19.93 11.95 40.94 3.51
3507 4324 1.134848 GGTGTCTGAGACTCTCATGGC 60.135 57.143 14.42 6.25 39.92 4.40
3508 4325 0.813821 TGTCTGAGACTCTCATGGCG 59.186 55.000 14.42 0.00 39.92 5.69
3527 4344 3.195698 GGCAAGGCTACGGCTTCG 61.196 66.667 0.00 0.00 45.21 3.79
3528 4345 2.125673 GCAAGGCTACGGCTTCGA 60.126 61.111 0.00 0.00 45.21 3.71
3530 4347 1.080093 CAAGGCTACGGCTTCGACA 60.080 57.895 0.00 0.00 45.21 4.35
3545 4364 3.826236 TCGACAAGAAGAACCTCGTAG 57.174 47.619 0.00 0.00 0.00 3.51
3551 4370 2.022195 AGAAGAACCTCGTAGCGCATA 58.978 47.619 11.47 0.00 0.00 3.14
3564 4383 1.952635 CGCATATCGCTGCAGCTCA 60.953 57.895 34.22 21.94 42.40 4.26
3568 4387 2.388890 ATATCGCTGCAGCTCACCCC 62.389 60.000 34.22 6.15 39.32 4.95
3593 4412 3.965292 ACGTAGTCGGACATCATGTAG 57.035 47.619 11.27 0.00 29.74 2.74
3594 4413 3.276857 ACGTAGTCGGACATCATGTAGT 58.723 45.455 11.27 0.00 29.74 2.73
3595 4414 3.693085 ACGTAGTCGGACATCATGTAGTT 59.307 43.478 11.27 0.00 29.74 2.24
3596 4415 4.035684 CGTAGTCGGACATCATGTAGTTG 58.964 47.826 11.27 0.00 0.00 3.16
3597 4416 4.438336 CGTAGTCGGACATCATGTAGTTGT 60.438 45.833 11.27 0.00 32.96 3.32
3598 4417 4.111375 AGTCGGACATCATGTAGTTGTC 57.889 45.455 11.27 10.36 43.24 3.18
3603 4422 3.845178 GACATCATGTAGTTGTCCGTGA 58.155 45.455 0.00 0.00 39.82 4.35
3604 4423 3.849911 ACATCATGTAGTTGTCCGTGAG 58.150 45.455 0.00 0.00 30.65 3.51
3605 4424 2.363788 TCATGTAGTTGTCCGTGAGC 57.636 50.000 0.00 0.00 0.00 4.26
3606 4425 1.616374 TCATGTAGTTGTCCGTGAGCA 59.384 47.619 0.00 0.00 0.00 4.26
3607 4426 1.995484 CATGTAGTTGTCCGTGAGCAG 59.005 52.381 0.00 0.00 0.00 4.24
3608 4427 0.317160 TGTAGTTGTCCGTGAGCAGG 59.683 55.000 0.00 0.00 0.00 4.85
3609 4428 0.317479 GTAGTTGTCCGTGAGCAGGT 59.683 55.000 0.00 0.00 0.00 4.00
3610 4429 1.045407 TAGTTGTCCGTGAGCAGGTT 58.955 50.000 0.00 0.00 0.00 3.50
3615 4928 2.197605 TCCGTGAGCAGGTTGACGA 61.198 57.895 6.68 0.00 33.64 4.20
3622 4935 0.250338 AGCAGGTTGACGAAGAACCC 60.250 55.000 10.16 0.00 43.52 4.11
3627 4940 0.531311 GTTGACGAAGAACCCCGTGT 60.531 55.000 0.00 0.00 39.30 4.49
3628 4941 1.039068 TTGACGAAGAACCCCGTGTA 58.961 50.000 0.00 0.00 39.30 2.90
3632 4945 0.172803 CGAAGAACCCCGTGTAGGAG 59.827 60.000 0.00 0.00 45.00 3.69
3669 4982 0.299895 CATTGACATGACGCTCGCTC 59.700 55.000 0.00 0.00 31.07 5.03
3671 4984 2.153547 TTGACATGACGCTCGCTCCA 62.154 55.000 0.00 0.00 0.00 3.86
3672 4985 1.875813 GACATGACGCTCGCTCCAG 60.876 63.158 0.00 0.00 0.00 3.86
3761 5080 3.746949 CTCGGTGCATGAGAGGGCC 62.747 68.421 12.24 0.00 35.43 5.80
3771 5090 3.181483 GCATGAGAGGGCCATAAAACTTG 60.181 47.826 6.18 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 1.602323 CCAAAGTAGCGCCCCAACA 60.602 57.895 2.29 0.00 0.00 3.33
273 274 2.158959 GTCTCGTTCATGCGGTCGG 61.159 63.158 0.00 0.00 0.00 4.79
324 325 4.776322 CCGACATCCCTTGCCGCA 62.776 66.667 0.00 0.00 28.71 5.69
362 363 5.680665 GCATCAAGGCAAAAGCTAGCTAAAT 60.681 40.000 19.70 4.60 0.00 1.40
441 442 0.904649 AACAGTCATCGAGCCCATGA 59.095 50.000 0.00 0.00 0.00 3.07
465 467 8.567948 CACACAGATAAAGTCTTACAAACCAAT 58.432 33.333 0.00 0.00 34.00 3.16
592 595 6.210584 TCCTGTTTTTCCTTGATAAATGGGAC 59.789 38.462 0.00 0.00 0.00 4.46
593 596 6.210584 GTCCTGTTTTTCCTTGATAAATGGGA 59.789 38.462 0.00 0.00 0.00 4.37
639 643 5.434408 TGATCCATCAAGACAAGAGAATGG 58.566 41.667 0.00 0.00 33.08 3.16
665 669 1.326852 CTAGTGCAGCGCAGAAAGATG 59.673 52.381 11.47 0.00 40.08 2.90
666 670 1.205655 TCTAGTGCAGCGCAGAAAGAT 59.794 47.619 11.47 0.00 40.08 2.40
667 671 0.603065 TCTAGTGCAGCGCAGAAAGA 59.397 50.000 11.47 1.26 40.08 2.52
828 832 6.018098 CCTTTCAGATGATGTGTAGATTCAGC 60.018 42.308 0.00 0.00 0.00 4.26
870 874 4.137543 AGGGCAACTGAAACTCTACTTTG 58.862 43.478 0.00 0.00 0.00 2.77
1014 1018 1.138069 GGCAGAGGAGGAAGAACTAGC 59.862 57.143 0.00 0.00 0.00 3.42
1015 1019 2.461695 TGGCAGAGGAGGAAGAACTAG 58.538 52.381 0.00 0.00 0.00 2.57
1019 1023 1.207791 GGATGGCAGAGGAGGAAGAA 58.792 55.000 0.00 0.00 0.00 2.52
1134 1144 3.019564 GGATTGGTTTGTGGATGGAGAG 58.980 50.000 0.00 0.00 0.00 3.20
1486 1496 4.812476 CGCGCCGATGAACTCCCA 62.812 66.667 0.00 0.00 0.00 4.37
1612 1622 1.492176 CTCCATGGCCCAGTTAGTGAT 59.508 52.381 6.96 0.00 0.00 3.06
1719 1729 2.203728 ACCGGGCAGTACACCTGA 60.204 61.111 6.32 0.00 44.49 3.86
1723 1733 2.431942 CACGACCGGGCAGTACAC 60.432 66.667 8.76 0.00 0.00 2.90
1842 1852 0.678366 ACTGGATGACGCTCTCGAGT 60.678 55.000 13.13 0.00 39.41 4.18
1904 1914 1.054574 TATGTTGTCGACGTTGACGC 58.945 50.000 26.73 22.04 44.43 5.19
1949 1959 5.416639 AGTGCAGTTCTTGATTAATGCATGA 59.583 36.000 0.00 0.00 44.55 3.07
1998 2008 1.163420 TCACGTCGCACCTGCAAATT 61.163 50.000 0.00 0.00 42.21 1.82
1999 2009 0.955428 ATCACGTCGCACCTGCAAAT 60.955 50.000 0.00 0.00 42.21 2.32
2000 2010 0.319986 TATCACGTCGCACCTGCAAA 60.320 50.000 0.00 0.00 42.21 3.68
2001 2011 1.011968 GTATCACGTCGCACCTGCAA 61.012 55.000 0.00 0.00 42.21 4.08
2157 2167 1.305549 GACCTCCTGGACGGGGTTA 60.306 63.158 7.47 0.00 36.73 2.85
2223 2233 2.863853 CGACACGCTGATGCCGATG 61.864 63.158 0.00 0.00 35.36 3.84
2313 2323 3.072476 TGGAGGAACCAGCTGAGC 58.928 61.111 17.39 0.00 44.64 4.26
2412 2422 2.433004 GGGCTGGTGTACCGGTTT 59.567 61.111 15.04 0.00 44.34 3.27
2529 2539 2.598565 CCCTTGATCTCCCACTCGATA 58.401 52.381 0.00 0.00 0.00 2.92
2532 2542 0.687757 TCCCCTTGATCTCCCACTCG 60.688 60.000 0.00 0.00 0.00 4.18
2550 2560 2.900546 CCAGTAGGTGACCCATATCCTC 59.099 54.545 0.00 0.00 0.00 3.71
2623 2633 3.499050 GGTGAGATGCAGCAGCTG 58.501 61.111 20.23 18.93 44.31 4.24
2673 2684 6.430308 GGTGACCATTCTATCAGTACGAGATA 59.570 42.308 0.00 9.68 0.00 1.98
2688 2699 2.403252 ATTCCTGACGGTGACCATTC 57.597 50.000 1.11 0.00 0.00 2.67
2696 2707 6.479972 TGATCAGTAAATATTCCTGACGGT 57.520 37.500 16.00 5.21 38.00 4.83
2741 2752 6.339194 TGATCGTGAAAATAACATACACCG 57.661 37.500 0.00 0.00 0.00 4.94
2744 2755 7.550906 TCACCATGATCGTGAAAATAACATACA 59.449 33.333 16.77 0.00 37.31 2.29
2760 2771 7.011202 CAGTGCTAGCATATTATCACCATGATC 59.989 40.741 22.51 1.07 38.26 2.92
2786 2797 5.527582 TGCTTTACTTTTCACTTCTCAGTCC 59.472 40.000 0.00 0.00 0.00 3.85
2837 2851 2.644299 TGGGTTCATCTTCAGGTCACAT 59.356 45.455 0.00 0.00 0.00 3.21
2891 2905 5.408604 ACTGTTGACTCCGTATCATGTTTTC 59.591 40.000 0.00 0.00 0.00 2.29
2917 2931 3.315191 TGGCGACAGGAAAAGAAAAAGAG 59.685 43.478 0.00 0.00 35.01 2.85
2918 2932 3.283751 TGGCGACAGGAAAAGAAAAAGA 58.716 40.909 0.00 0.00 35.01 2.52
2919 2933 3.708563 TGGCGACAGGAAAAGAAAAAG 57.291 42.857 0.00 0.00 35.01 2.27
2961 3775 3.391665 CTGTAGGCTTGCCTCGGGG 62.392 68.421 18.28 0.00 0.00 5.73
2997 3812 4.123545 AATACACCGGGGCTGGCC 62.124 66.667 12.58 12.58 0.00 5.36
2999 3814 2.828549 GCAATACACCGGGGCTGG 60.829 66.667 1.73 0.00 0.00 4.85
3001 3816 2.045340 GTGCAATACACCGGGGCT 60.045 61.111 1.73 0.00 44.02 5.19
3030 3845 1.901948 AACTCCAGTCACGCTCGGA 60.902 57.895 0.00 0.00 0.00 4.55
3032 3847 0.318699 TTCAACTCCAGTCACGCTCG 60.319 55.000 0.00 0.00 0.00 5.03
3033 3848 1.269831 ACTTCAACTCCAGTCACGCTC 60.270 52.381 0.00 0.00 0.00 5.03
3034 3849 0.753262 ACTTCAACTCCAGTCACGCT 59.247 50.000 0.00 0.00 0.00 5.07
3035 3850 2.433868 TACTTCAACTCCAGTCACGC 57.566 50.000 0.00 0.00 0.00 5.34
3036 3851 5.465390 TCAAAATACTTCAACTCCAGTCACG 59.535 40.000 0.00 0.00 0.00 4.35
3037 3852 6.861065 TCAAAATACTTCAACTCCAGTCAC 57.139 37.500 0.00 0.00 0.00 3.67
3038 3853 9.739276 AATATCAAAATACTTCAACTCCAGTCA 57.261 29.630 0.00 0.00 0.00 3.41
3040 3855 8.883731 CGAATATCAAAATACTTCAACTCCAGT 58.116 33.333 0.00 0.00 0.00 4.00
3041 3856 9.098355 TCGAATATCAAAATACTTCAACTCCAG 57.902 33.333 0.00 0.00 0.00 3.86
3042 3857 9.443323 TTCGAATATCAAAATACTTCAACTCCA 57.557 29.630 0.00 0.00 0.00 3.86
3065 3880 2.669391 GCTGCTTGGGTTCTCATTTTCG 60.669 50.000 0.00 0.00 0.00 3.46
3084 3899 3.951775 ATCGTCAAGACAGAAAGAGCT 57.048 42.857 0.72 0.00 0.00 4.09
3134 3950 1.407258 CTTTGTGTTCTTTTCGCCCCA 59.593 47.619 0.00 0.00 0.00 4.96
3135 3951 1.679153 TCTTTGTGTTCTTTTCGCCCC 59.321 47.619 0.00 0.00 0.00 5.80
3141 3957 7.239763 TCCCTTTTCTTCTTTGTGTTCTTTT 57.760 32.000 0.00 0.00 0.00 2.27
3145 3961 4.339530 AGCTCCCTTTTCTTCTTTGTGTTC 59.660 41.667 0.00 0.00 0.00 3.18
3149 3965 5.311844 AGTAGCTCCCTTTTCTTCTTTGT 57.688 39.130 0.00 0.00 0.00 2.83
3220 4037 4.082733 GGATCTTAGTTTCTTTGGTGCCAC 60.083 45.833 0.00 0.00 0.00 5.01
3222 4039 4.079253 TGGATCTTAGTTTCTTTGGTGCC 58.921 43.478 0.00 0.00 0.00 5.01
3242 4059 4.044336 TGGCGCATAAGAATTTGATTGG 57.956 40.909 10.83 0.00 0.00 3.16
3268 4085 3.492102 TTGTGTGCTTTTAGCCTCTCT 57.508 42.857 0.00 0.00 41.51 3.10
3269 4086 3.057946 CCTTTGTGTGCTTTTAGCCTCTC 60.058 47.826 0.00 0.00 41.51 3.20
3270 4087 2.887152 CCTTTGTGTGCTTTTAGCCTCT 59.113 45.455 0.00 0.00 41.51 3.69
3271 4088 2.623416 ACCTTTGTGTGCTTTTAGCCTC 59.377 45.455 0.00 0.00 41.51 4.70
3283 4100 4.161102 AGAGTAGCCTCTTACCTTTGTGT 58.839 43.478 0.00 0.00 46.08 3.72
3290 4107 3.083293 CCGGATAGAGTAGCCTCTTACC 58.917 54.545 0.00 2.52 46.08 2.85
3291 4108 3.753815 ACCGGATAGAGTAGCCTCTTAC 58.246 50.000 9.46 0.00 46.08 2.34
3292 4109 4.142790 CAACCGGATAGAGTAGCCTCTTA 58.857 47.826 9.46 0.00 46.08 2.10
3307 4124 1.006805 CATTTTTGGCGCAACCGGA 60.007 52.632 9.46 0.00 43.94 5.14
3334 4151 2.625790 CCGCATAGAGTAGCTCCTTCTT 59.374 50.000 0.00 0.00 0.00 2.52
3335 4152 2.235016 CCGCATAGAGTAGCTCCTTCT 58.765 52.381 0.00 0.00 0.00 2.85
3336 4153 1.957877 ACCGCATAGAGTAGCTCCTTC 59.042 52.381 0.00 0.00 0.00 3.46
3357 4174 3.190535 TGAATCTTAGTTTCTTTGGCGCC 59.809 43.478 22.73 22.73 0.00 6.53
3359 4176 5.154222 GGTTGAATCTTAGTTTCTTTGGCG 58.846 41.667 4.89 0.00 0.00 5.69
3402 4219 1.762370 CCCCTTCCTTTTGTGTGCTTT 59.238 47.619 0.00 0.00 0.00 3.51
3403 4220 1.413118 CCCCTTCCTTTTGTGTGCTT 58.587 50.000 0.00 0.00 0.00 3.91
3437 4254 0.035458 GGAAGGGGATACTCCATGCG 59.965 60.000 0.00 0.00 38.59 4.73
3440 4257 4.909284 ACTAAAGGAAGGGGATACTCCAT 58.091 43.478 0.00 0.00 38.59 3.41
3445 4262 4.595986 TGCAAACTAAAGGAAGGGGATAC 58.404 43.478 0.00 0.00 0.00 2.24
3447 4264 3.564352 CCTGCAAACTAAAGGAAGGGGAT 60.564 47.826 0.00 0.00 32.43 3.85
3476 4293 3.131933 GTCTCAGACACCAGCTGTATCAT 59.868 47.826 13.81 0.00 34.98 2.45
3507 4324 3.665675 AAGCCGTAGCCTTGCCTCG 62.666 63.158 0.00 0.00 41.25 4.63
3508 4325 1.815840 GAAGCCGTAGCCTTGCCTC 60.816 63.158 0.00 0.00 41.25 4.70
3525 4342 2.095364 GCTACGAGGTTCTTCTTGTCGA 60.095 50.000 0.00 0.00 33.70 4.20
3527 4344 2.251893 CGCTACGAGGTTCTTCTTGTC 58.748 52.381 0.00 0.00 33.70 3.18
3528 4345 1.669211 GCGCTACGAGGTTCTTCTTGT 60.669 52.381 0.00 0.00 35.67 3.16
3530 4347 0.601558 TGCGCTACGAGGTTCTTCTT 59.398 50.000 9.73 0.00 0.00 2.52
3551 4370 4.479993 GGGGTGAGCTGCAGCGAT 62.480 66.667 31.78 17.08 45.82 4.58
3568 4387 0.381089 GATGTCCGACTACGTCAGGG 59.619 60.000 0.00 0.00 35.78 4.45
3569 4388 1.092348 TGATGTCCGACTACGTCAGG 58.908 55.000 0.00 0.00 39.80 3.86
3570 4389 2.097629 ACATGATGTCCGACTACGTCAG 59.902 50.000 0.00 0.00 45.84 3.51
3571 4390 2.089201 ACATGATGTCCGACTACGTCA 58.911 47.619 0.00 9.03 46.49 4.35
3572 4391 2.846039 ACATGATGTCCGACTACGTC 57.154 50.000 0.00 0.00 37.88 4.34
3573 4392 3.276857 ACTACATGATGTCCGACTACGT 58.723 45.455 0.00 0.00 37.88 3.57
3574 4393 3.965292 ACTACATGATGTCCGACTACG 57.035 47.619 0.00 0.00 39.43 3.51
3575 4394 4.995124 ACAACTACATGATGTCCGACTAC 58.005 43.478 0.00 0.00 0.00 2.73
3576 4395 5.244785 GACAACTACATGATGTCCGACTA 57.755 43.478 0.00 0.00 41.00 2.59
3577 4396 4.111375 GACAACTACATGATGTCCGACT 57.889 45.455 0.00 0.00 41.00 4.18
3582 4401 3.845178 TCACGGACAACTACATGATGTC 58.155 45.455 0.00 8.28 44.54 3.06
3583 4402 3.849911 CTCACGGACAACTACATGATGT 58.150 45.455 2.65 2.65 34.26 3.06
3584 4403 2.604914 GCTCACGGACAACTACATGATG 59.395 50.000 0.00 0.00 0.00 3.07
3585 4404 2.233676 TGCTCACGGACAACTACATGAT 59.766 45.455 0.00 0.00 0.00 2.45
3586 4405 1.616374 TGCTCACGGACAACTACATGA 59.384 47.619 0.00 0.00 0.00 3.07
3587 4406 1.995484 CTGCTCACGGACAACTACATG 59.005 52.381 0.00 0.00 0.00 3.21
3588 4407 1.066858 CCTGCTCACGGACAACTACAT 60.067 52.381 0.00 0.00 0.00 2.29
3589 4408 0.317160 CCTGCTCACGGACAACTACA 59.683 55.000 0.00 0.00 0.00 2.74
3590 4409 0.317479 ACCTGCTCACGGACAACTAC 59.683 55.000 0.00 0.00 0.00 2.73
3591 4410 1.045407 AACCTGCTCACGGACAACTA 58.955 50.000 0.00 0.00 0.00 2.24
3592 4411 0.532862 CAACCTGCTCACGGACAACT 60.533 55.000 0.00 0.00 0.00 3.16
3593 4412 0.531974 TCAACCTGCTCACGGACAAC 60.532 55.000 0.00 0.00 0.00 3.32
3594 4413 0.531974 GTCAACCTGCTCACGGACAA 60.532 55.000 0.00 0.00 0.00 3.18
3595 4414 1.069090 GTCAACCTGCTCACGGACA 59.931 57.895 0.00 0.00 0.00 4.02
3596 4415 2.022129 CGTCAACCTGCTCACGGAC 61.022 63.158 0.00 0.00 0.00 4.79
3597 4416 1.740332 TTCGTCAACCTGCTCACGGA 61.740 55.000 0.00 0.00 33.02 4.69
3598 4417 1.284982 CTTCGTCAACCTGCTCACGG 61.285 60.000 0.00 0.00 33.02 4.94
3599 4418 0.318699 TCTTCGTCAACCTGCTCACG 60.319 55.000 0.00 0.00 0.00 4.35
3600 4419 1.527311 GTTCTTCGTCAACCTGCTCAC 59.473 52.381 0.00 0.00 0.00 3.51
3601 4420 1.540363 GGTTCTTCGTCAACCTGCTCA 60.540 52.381 5.89 0.00 40.33 4.26
3602 4421 1.149148 GGTTCTTCGTCAACCTGCTC 58.851 55.000 5.89 0.00 40.33 4.26
3603 4422 0.250338 GGGTTCTTCGTCAACCTGCT 60.250 55.000 11.11 0.00 42.73 4.24
3604 4423 1.235281 GGGGTTCTTCGTCAACCTGC 61.235 60.000 11.11 0.00 42.73 4.85
3605 4424 0.949105 CGGGGTTCTTCGTCAACCTG 60.949 60.000 11.11 0.00 42.73 4.00
3606 4425 1.370064 CGGGGTTCTTCGTCAACCT 59.630 57.895 11.11 0.00 42.73 3.50
3607 4426 1.070275 ACGGGGTTCTTCGTCAACC 59.930 57.895 4.84 4.84 42.45 3.77
3608 4427 0.531311 ACACGGGGTTCTTCGTCAAC 60.531 55.000 0.00 0.00 37.53 3.18
3609 4428 1.000060 CTACACGGGGTTCTTCGTCAA 60.000 52.381 0.00 0.00 37.53 3.18
3610 4429 0.599558 CTACACGGGGTTCTTCGTCA 59.400 55.000 0.00 0.00 37.53 4.35
3615 4928 0.178912 ACCTCCTACACGGGGTTCTT 60.179 55.000 0.00 0.00 33.96 2.52
3622 4935 3.066190 TGCCGACCTCCTACACGG 61.066 66.667 0.00 0.00 46.74 4.94
3669 4982 1.595109 TGATGCCGATTAGCGCTGG 60.595 57.895 22.90 14.22 39.11 4.85
3671 4984 1.595382 GGTGATGCCGATTAGCGCT 60.595 57.895 17.26 17.26 39.11 5.92
3672 4985 2.939022 GGTGATGCCGATTAGCGC 59.061 61.111 0.00 0.00 39.11 5.92
3692 5011 1.153568 CACCATCTCGTGTGCCGAT 60.154 57.895 0.00 0.00 46.23 4.18
3706 5025 0.325933 CTTCATGCTCCTGGTCACCA 59.674 55.000 0.00 0.00 0.00 4.17
3746 5065 0.183492 TTATGGCCCTCTCATGCACC 59.817 55.000 0.00 0.00 0.00 5.01
3757 5076 7.158697 ACAAAAAGATACAAGTTTTATGGCCC 58.841 34.615 0.00 0.00 0.00 5.80


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.